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Martin McCullagh, Ph.D. - Publications

Affiliations: 
2010 Chemistry Northwestern University, Evanston, IL 
Area:
theory and computation as applies to problems in nanotechnology, properties of materials, macromolecular structures and dynamics, molecular self-assembly, optics, materials physics and biophysics
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Lawal MM, Roy P, McCullagh M. Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. The Journal of Physical Chemistry. B. PMID 38175211 DOI: 10.1021/acs.jpcb.3c06714  0.345
2023 Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. Biorxiv : the Preprint Server For Biology. PMID 38077049 DOI: 10.1101/2023.11.30.569434  0.33
2023 Lawal MM, Roy P, McCullagh M. The Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. Biorxiv : the Preprint Server For Biology. PMID 37808802 DOI: 10.1101/2023.09.28.560057  0.347
2023 Sasmal S, McCullagh M, Hocky GM. Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions. Journal of Chemical Theory and Computation. PMID 37130367 DOI: 10.1021/acs.jctc.3c00051  0.757
2022 Klem H, Hocky GM, McCullagh M. Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation. PMID 35483073 DOI: 10.1021/acs.jctc.1c01290  0.71
2021 Klem H, McCullagh M, Paton RS. Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Topics in Catalysis. 65: 165-186. PMID 36304771 DOI: 10.1007/s11244-021-01521-1  0.752
2021 Weber R, McCullagh M. Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase. The Journal of Physical Chemistry. B. 125: 8787-8796. PMID 34328740 DOI: 10.1021/acs.jpcb.1c04528  0.314
2020 Du Pont KE, Sexton NR, McCullagh M, Ebel GD, Geiss BJ. A Hyperactive Kunjin Virus NS3 Helicase Mutant Demonstrates Increased Dissemination and Mortality in Mosquitoes. Journal of Virology. PMID 32699093 DOI: 10.1128/Jvi.01021-20  0.333
2020 Lake PT, Davidson RB, Klem H, Hocky GM, McCullagh M. Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian. Journal of Chemical Theory and Computation. PMID 32251581 DOI: 10.1021/Acs.Jctc.9B01149  0.697
2020 Davidson RB, Hendrix J, Geiss BJ, McCullagh M. RNA-Dependent Structures of the RNA-Binding Loop in the Flavivirus NS3 Helicase. The Journal of Physical Chemistry. B. PMID 32105483 DOI: 10.1021/Acs.Jpcb.0C00457  0.773
2019 Du Pont KE, Davidson RB, McCullagh M, Geiss BJ. Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft. The Journal of Biological Chemistry. PMID 31914411 DOI: 10.1074/Jbc.Ra119.011922  0.777
2019 Remington JM, McCullagh M, Kohler B. Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics. The Journal of Physical Chemistry. B. PMID 30767498 DOI: 10.1021/Acs.Jpcb.8B12172  0.336
2019 Davidson RB, McCullagh M. Theoretical Modeling of the RNA-Enhanced NTPase Activity of Dengue and Zika NS3 Helicases Biophysical Journal. 116: 434a-435a. DOI: 10.1016/J.Bpj.2018.11.2340  0.72
2019 Davidson RB, McCullagh M. Lβ3β4 Conformations of the Flaviviridae NS3h Protein Biophysical Journal. 116: 434a. DOI: 10.1016/J.Bpj.2018.11.2339  0.706
2018 Votaw KA, McCullagh M. Characterization of the Search Complex and Recognition Mechanism of the AlkD DNA Glycosylase. The Journal of Physical Chemistry. B. PMID 30525620 DOI: 10.1021/Acs.Jpcb.8B09555  0.313
2018 Anderson J, Lake PT, McCullagh M. The Initial Aggregation and Ordering Mechanism of Diphenylalanine From Microsecond All-Atom Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 30511861 DOI: 10.1021/Acs.Jpcb.8B10335  0.334
2018 Mattson MA, Green TD, Lake PT, McCullagh M, Krummel AT. Elucidating Structural Evolution of Perylene Diimide Aggregates Using Vibrational Spectroscopy and Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 29683669 DOI: 10.1021/Acs.Jpcb.8B02355  0.334
2018 Davidson RB, Hendrix J, Geiss BJ, McCullagh M. Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations. Plos Computational Biology. 14: e1006103. PMID 29659571 DOI: 10.1371/Journal.Pcbi.1006103  0.79
2018 Du Pont KE, Davidson RB, Geiss BJ, McCullagh M. Molecular Analysis of Dengue NS3 Helicase Function Biophysical Journal. 114: 233a. DOI: 10.1016/J.Bpj.2017.11.1299  0.707
2017 Lake PT, McCullagh M. IS-SPA: An Implicit Treatment of the Non-polar Component to Solvation for Simulating Molecular Aggregation. Journal of Chemical Theory and Computation. PMID 29120632 DOI: 10.1021/Acs.Jctc.7B00698  0.35
2017 Davidson RB, Geiss BJ, McCullagh M. Molecular Allostery in Dengue NS3 Helicase along the ATP Hydrolysis Cycle Biophysical Journal. 112: 497a. DOI: 10.1016/J.Bpj.2016.11.2689  0.75
2016 McCullagh P, Lake PT, McCullagh M. Deriving Coarse-grained Charges from All-atom Systems: An Analytic Solution. Journal of Chemical Theory and Computation. PMID 27541500 DOI: 10.1021/Acs.Jctc.6B00507  0.312
2016 McCullagh M, Davidson R. The Coupling of ATP Hydrolysis to RNA Translocation in Dengue Virus NS3 Helicase: Insights from Molecular Dynamics Biophysical Journal. 110: 381a. DOI: 10.1016/J.Bpj.2015.11.2059  0.749
2015 Baker JL, Courtemanche N, Parton DL, McCullagh M, Pollard TD, Voth GA. Electrostatic interactions between the Bni1p Formin FH2 domain and actin influence actin filament nucleation. Structure (London, England : 1993). 23: 68-79. PMID 25482541 DOI: 10.1016/J.Str.2014.10.014  0.497
2015 Baker JL, Courtemanche N, Parton DL, McCullagh M, Pollard TD, Voth GA. Actin Filament Nucleation is Influenced by Electrostatic Interactions with the Bni1p Formin FH2 Domain Biophysical Journal. 108: 508a. DOI: 10.1016/J.Bpj.2014.11.2782  0.497
2014 McCullagh M, Saunders MG, Voth GA. Unraveling the mystery of ATP hydrolysis in actin filaments. Journal of the American Chemical Society. 136: 13053-8. PMID 25181471 DOI: 10.1021/Ja507169F  0.659
2014 Hariharan M, Siegmund K, Saurel C, McCullagh M, Schatz GC, Lewis FD. Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 13: 266-71. PMID 24212351 DOI: 10.1039/C3Pp50283J  0.45
2014 Neelakandan PP, Zeidan TA, McCullagh M, Schatz GC, Vura-Weis J, Kim CH, Wasielewski MR, Lewis FD. Ground and excited state electronic spectra of perylenediimide dimers with flexible and rigid geometries in DNA conjugates Chemical Science. 5: 973-981. DOI: 10.1039/C3Sc52908H  0.447
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The Theory of Ultra-Coarse-Graining. 1. General Principles. Journal of Chemical Theory and Computation. 9: 2466-80. PMID 26583735 DOI: 10.1021/Ct4000444  0.759
2013 McCullagh M, Voth GA. Unraveling the role of the protein environment for [FeFe]-hydrogenase: a new application of coarse-graining. The Journal of Physical Chemistry. B. 117: 4062-71. PMID 23484958 DOI: 10.1021/Jp402441S  0.497
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The theory of ultra-coarse-graining. 1. General principles Journal of Chemical Theory and Computation. 9: 2466-2480. DOI: 10.1021/ct4000444  0.702
2012 Neelakandan PP, McCullagh M, Schatz GC, Lewis FD. Electronic interactions in helical stacked arrays of the modified DNA base pyrrolocytosine. The Journal of Physical Chemistry. B. 116: 5199-204. PMID 22486518 DOI: 10.1021/Jp302385C  0.409
2012 McCullagh M, Franco I, Ratner MA, Schatz GC. Defects in DNA: Lessons from molecular motor design Journal of Physical Chemistry Letters. 3: 689-693. DOI: 10.1021/Jz201649K  0.458
2012 Pan Z, Hariharan M, Arkin JD, Jalilov AS, McCullagh M, Schatz GC, Lewis FD. Erratum: Electron donor-acceptor interactions with flanking purines influence the efficiency of thymine photodimerization (Journal of the American Chemical Society (2011) 133 (20793-20798) DOI: 10.1021/ja205460f) Journal of the American Chemical Society. 134. DOI: 10.1021/Ja2117156  0.37
2011 Pan Z, Hariharan M, Arkin JD, Jalilov AS, McCullagh M, Schatz GC, Lewis FD. Electron donor-acceptor interactions with flanking purines influence the efficiency of thymine photodimerization. Journal of the American Chemical Society. 133: 20793-8. PMID 22032333 DOI: 10.1021/Ja205460F  0.486
2011 McCullagh M, Franco I, Ratner MA, Schatz GC. DNA-based optomechanical molecular motor. Journal of the American Chemical Society. 133: 3452-9. PMID 21341796 DOI: 10.1021/Ja109071A  0.713
2011 Pan Z, McCullagh M, Schatz GC, Lewis FD. Conformational control of thymine photodimerization in purine-containing trinucleotides Journal of Physical Chemistry Letters. 2: 1432-1438. DOI: 10.1021/Jz200532W  0.458
2010 Hariharan M, McCullagh M, Schatz GC, Lewis FD. Conformational control of thymine photodimerization in single-strand and duplex DNA containing locked nucleic acid TT steps. Journal of the American Chemical Society. 132: 12856-8. PMID 20735128 DOI: 10.1021/Ja106203Q  0.452
2010 McCullagh M, Hariharan M, Lewis FD, Markovitsi D, Douki T, Schatz GC. Conformational control of TT dimerization in DNA conjugates. A molecular dynamics study. The Journal of Physical Chemistry. B. 114: 5215-21. PMID 20307059 DOI: 10.1021/Jp100983T  0.49
2010 Hariharan M, McCullagh M, Schatz GC, Lewis FD. Erratum: Conformational control of thymine photodimerization in single-strand and duplex DNA containing locked nucleic acid TT steps (Journal of the American Chemical Society (2010) 132 (12856-12858)) Journal of the American Chemical Society. 132. DOI: 10.1021/Ja108528Q  0.423
2008 McCullagh M, Zhang L, Karaba AH, Zhu H, Schatz GC, Lewis FD. Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates. The Journal of Physical Chemistry. B. 112: 11415-21. PMID 18707160 DOI: 10.1021/Jp802378A  0.466
2008 McCullagh M, Prytkova T, Tonzani S, Winter ND, Schatz GC. Modeling self-assembly processes driven by nonbonded interactions in soft materials. The Journal of Physical Chemistry. B. 112: 10388-98. PMID 18636770 DOI: 10.1021/Jp803192U  0.749
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